This is a rough draft of a book that is intended to gather as much as I know on this topic. It will be used in graduate courses and workshops.
The actual .pdf is in book/main.pdf
There is much to be done, including code-checking and polishing.
There are not many use examples. Check out the Macklaim 2013 paper for meta-transcriptomics, the Bian 2017 paper for 16S rRNA gene sequencing and the Gloor 2017 Frontiers paper for additional code.
Please send comments if you have them